Support TPR files produced by gromacs 2023 (MDAnalysis#4052)

* Add test TPR files for gromacs 2023

* Allow tpx version 129

These files are produced by gromacs 2023. Note that we only allow the
tpx version here. We do not implement any of the changes to the tpr
format.

* Update changelog to account for TPR 129

* Update the documentation to account for tpx 129

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 ------------------------------------------------------------------------------
 
 ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
-         ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler
+         ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud
  * 2.5.0
 
 Fixes
@@ -28,6 +28,7 @@ Fixes
     (Issue #3336)
 
 Enhancements
+  * Add support for TPR files produced by Gromacs 2023 (Issue #4047)
   * Add distopia distance calculation library bindings as a selectable backend
     for `calc_bonds` in `MDA.lib.distances`. (Issue #3783, PR #3914)
   * AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)

package/MDAnalysis/topology/TPRParser.py

@@ -65,6 +65,7 @@
    119        27             2020[*]_             yes
    122        28             2021                 yes
    127        28             2022                 yes
+   129        28             2023                 yes
    ========== ============== ==================== =====
 
 .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.

package/MDAnalysis/topology/tpr/setting.py

@@ -38,7 +38,7 @@
 """
 
 #: Gromacs TPR file format versions that can be read by the TPRParser.
-SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127)
+SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127, 129)
 
 # Some constants
 STRLEN = 4096

testsuite/MDAnalysisTests/datafiles.py

@@ -81,13 +81,14 @@
     "TPR450", "TPR451", "TPR452", "TPR453", "TPR454", "TPR455", "TPR455Double",
     "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016",
     "TPR2018", "TPR2019B3", "TPR2020B2", "TPR2020", "TPR2020Double",
-    "TPR2021", "TPR2021Double", "TPR2022RC1",
+    "TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023",
     "TPR510_bonded", "TPR2016_bonded", "TPR2018_bonded", "TPR2019B3_bonded",
     "TPR2020B2_bonded", "TPR2020_bonded", "TPR2020_double_bonded",
     "TPR2021_bonded", "TPR2021_double_bonded", "TPR2022RC1_bonded",
-    "TPR334_bonded",
+    "TPR334_bonded", "TPR2023_bonded",
     "TPR_EXTRA_2021", "TPR_EXTRA_2020", "TPR_EXTRA_2018",
     "TPR_EXTRA_2016", "TPR_EXTRA_407", "TPR_EXTRA_2022RC1",
+    "TPR_EXTRA_2023",
     "PDB_sub_sol", "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
     "XTC_sub_sol",
@@ -383,6 +384,7 @@
 TPR2020 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2020.tpr')
 TPR2021 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2021.tpr')
 TPR2022RC1 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2022-rc1.tpr')
+TPR2023 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2023.tpr')
 # double precision
 TPR455Double = resource_filename(__name__, 'data/tprs/drew_gmx_4.5.5.double.tpr')
 TPR460 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.tpr')
@@ -401,7 +403,9 @@
 TPR2021_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2021.tpr')
 TPR2021_double_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2021_double.tpr')
 TPR2022RC1_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2022-rc1.tpr')
+TPR2023_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2023.tpr')
 # all interactions
+TPR_EXTRA_2023 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2023.tpr')
 TPR_EXTRA_2022RC1 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2022-rc1.tpr')
 TPR_EXTRA_2021 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2021.tpr')
 TPR_EXTRA_2020 = resource_filename(__name__, 'data/tprs/virtual_sites/extra-interactions-2020.tpr')

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -32,13 +32,14 @@
     TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double,
     TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR510_bonded,
     TPR2016, TPR2018, TPR2019B3, TPR2020B2, TPR2020, TPR2020Double,
-    TPR2021, TPR2021Double, TPR2022RC1,
+    TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
     TPR2016_bonded, TPR2018_bonded, TPR2019B3_bonded,
     TPR2020B2_bonded, TPR2020_bonded, TPR2020_double_bonded,
     TPR2021_bonded, TPR2021_double_bonded, TPR334_bonded,
-    TPR2022RC1_bonded,
+    TPR2022RC1_bonded, TPR2023_bonded,
     TPR_EXTRA_2021, TPR_EXTRA_2020, TPR_EXTRA_2018,
     TPR_EXTRA_2016, TPR_EXTRA_407, TPR_EXTRA_2022RC1,
+    TPR_EXTRA_2023,
     XTC,
 )
 from MDAnalysisTests.topology.base import ParserBase
@@ -55,6 +56,8 @@
     TPR2020_bonded,
     TPR2020_double_bonded,
     TPR2022RC1_bonded,
+    TPR2023_bonded,
+    TPR_EXTRA_2023,
     TPR_EXTRA_2022RC1,
     TPR_EXTRA_2021,
     TPR_EXTRA_2020,
@@ -111,7 +114,7 @@ class TestTPRGromacsVersions(TPRAttrs):
                             TPR407, TPR450, TPR451, TPR452, TPR453, TPR454,
                             TPR455, TPR502, TPR504, TPR505, TPR510, TPR2016,
                             TPR2018, TPR2019B3, TPR2020, TPR2020Double,
-                            TPR2021, TPR2021Double, TPR2022RC1])
+                            TPR2021, TPR2021Double, TPR2022RC1, TPR2023,])
     def filename(self, request):
         return request.param
 
@@ -238,6 +241,7 @@ def test_all_impropers(topology, impr):
 @pytest.fixture(params=(
     TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, TPR450, TPR451,
     TPR452, TPR453, TPR454, TPR502, TPR504, TPR505, TPR510, TPR2016, TPR2018,
+    TPR2023,
 ))
 def bonds_water(request):
     parser = MDAnalysis.topology.TPRParser.TPRParser(request.param).parse()